On Mon, Jun 29, 2009 at 11:30 AM, Mohamed Lajnef
<Mohamed.lajnef@inserm.fr>wrote:

> Dearr Sean,
>
> thank you for you quik answer, i use Illumina file  and i have another
> question about normalization within arrays, can i use  normalizeWithinArrays
> (lowess method) from Limma package ?


No.  NormalizeWithinArrays is for two-color data.  You might want to look at
using the lumi or beadarray packages, as they are specifically designed to
work with Illumina data.

Sean


>
>
> Sean Davis a écrit :
>
>
>>
>> On Mon, Jun 29, 2009 at 11:12 AM, Mohamed Lajnef <
>> Mohamed.lajnef@inserm.fr <mailto:Mohamed.lajnef@inserm.fr>> wrote:
>>
>>    Daer all,
>>
>>    I need to use a filtering tools for my data, but i dont know  if i
>>    use my filtering tools after or before normalization, which is better?
>>
>>
>> Normally, filtering is applied after normalization, but it will
>> potentially depend on the array type, the array content, and the
>> normalization method you wish to apply.
>>
>> Sean
>>
>>
>
>
> --
> Mohamed Lajnef
> INSERM Unité 955. 40 rue de Mesly. 94000 Créteil.
> Courriel : Mohamed.lajnef@inserm.fr tel. : 01 49 81 31 31 (poste 18470)
> Sec : 01 49 81 32 90
> fax : 01 49 81 30 99
>

	[[alternative HTML version deleted]]

